Biology subjects

Tumeo, A.

Publications and source records attributed to Tumeo, A..

4 recordsLinked to original sources

bioRxiv2026

Single-time-point shotgun metagenomics of four Irish Integrated Constructed Wetlands reveals microbial dynamics in wastewater treatment.

Over the past 20 years, the Integrated Constructed Wetland (ICW) concept has been applied in Ireland for wastewater treatment, offering a nature-based solution for reducing pollutants and antimicrobial resistance genes (ARGs) in effluents and receiving environments. However, wastewater microbial communities remain inadequately characterized and their dynamics across treatment largely unexplored. Here, we present a culture-independent investigation of four Irish ICWs, aiming to advance our understanding of microbial dynamics in wastewater treatment. Shotgun metagenomic sequencing was conducted on influent and effluent samples collected in biological triplicates from four ICWs treating agricultural, companion animal, industrial, and municipal wastewater, alongside eight positive and ten negative controls for filtering and sequencing. End-to-end metagenomic analysis was performed with SqueezeMeta. Taxonomic placement of high-quality metagenome-assembled-genomes (HQ-MAGs) was confirmed with GTDB-Tk. Decontamination and statistical analyses were conducted in R. Coassembled contigs were screened for ARGs, virulence- and plasmid-associated sequences. Results revealed statistically significant shifts in taxonomic and functional profiles across treatment. Effluent populations exhibited generally higher richness than corresponding influents, yet were more similar to one another across locations. Multi-log-scale increases were observed in the relative abundance of environmental genera (Legionella, Methylotenera, Thiothrix), alongside reductions in common faecal/human indicators (Bacteroides, Lactococcus, Prevotella), and up to 80% ARGs removal. Collectively, our findings provide insights into ICW efficacy, showing that they can drive marked shifts in wastewater microbiome and ARG reduction. Our culture-independent approach retrieved 34 HQ-MAGs, including 19 potentially novel taxa, uncovering previously uncharacterized microbial diversity that is potentially unique to the Irish environment and warrants further investigation.

microbiology↗

bioRxiv2025

Human colonization with Phytobacter co-harbouring blaIMP-4 and mcr-9.1 highlights its potential as emerging human pathogen.

Phytobacter is a recently delineated, frequently misidentified genus within the order Enterobacterales. Following two rare cases of patient colonization with multidrug resistant Phytobacter in Ireland, this study presents a genus-wide genomic analysis that aims to define the pathogenic potential of Phytobacter species, with emphasis on their role as emerging human pathogens and reservoirs of carbapenemases. Two carbapenemase-encoding isolates were recovered from rectal swabs in Ireland in 2024 and were initially identified as Phytobacter by MALDI-ToF. Whole-genome sequencing with in silico species typing (dDDH, ANI) provided definitive taxonomic resolution. A genus-wide maximum-likelihood core-genome phylogeny was reconstructed, and the plasmidome and resistome were bioinformatically profiled across all available Phytobacter genomes. Phenotypic susceptibility of the Irish isolates was determined through minimum inhibitory concentration (MIC) testing. The Irish isolates (P. diazotrophicus E787336 and P. ursingii E980862) are the first reported Phytobacter strains carrying both plasmid-borne blaIMP-4 and mcr-9.1 in the genus. MIC testing confirmed resistance to aztreonam, aminoglycosides, cephalosporins, fluoroquinolones, and the {beta}-lactam/{beta}-lactamase inhibitor combination piperacillin-tazobactam. Across 34 Phytobacter genomes examined, 22 distinct plasmid replicon types were identified in 22 isolates, often shared across species. The genus-wide resistome encompassed 71 genes, more than half predicted to be acquired, with carbapenemases detected in 26.5% (9/34) of the genomes. In summary, Phytobacter harbors a diverse, plasmid-borne resistome including carbapenemases, with documented cases of human colonization and infection. These findings support its recognition as an emerging pathogen and reservoir of antimicrobial resistance, underscoring the need for improved clinical identification, genomic surveillance, and preparedness for limited treatment options. Author summarySince Phytobacter was first characterized in 2007, this bacterial genus has mainly been associated with plant growth promotion. More recently, however, increasing reports of human infections have raised concerns about its potential as emerging bacterial pathogen. These are further underscored by the description of multidrug resistant isolates capable to withstand different classes of antimicrobials, including carbapenems which are often used as a last line of treatment. Following the rare finding of multidrug resistant Phytobacter in two patients in Ireland, we combined bioinformatics and laboratory testing to characterize the antimicrobial resistance profile of this overlooked bacterial genus. Our results uncover the variety of resistance determinants, including to carbapenems, which is encoded in the genomes of Phytobacter. This shows its potential as hidden reservoir of drug resistance and emerging bacterial pathogen. We encourage improved clinical recognition and monitoring of Phytobacter to better anticipate infections with limited therapeutic options.

genomics↗

bioRxiv2025

Plasmidome, resistome, and virulence-associated genes characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.

Evidence shows persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. This study aims to explore the mechanisms underpinning such adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASAs Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic profiling indicated the unique presence in PHSF-originating isolates of two complete efflux pumps and of a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. Observed ubiquity of blaOXA in investigated genomes (n=112) and phenotypically-validated multidrug-resistant profile of E154408A strain highlight A. johnsoniis potential as antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post initial isolation. ImportanceAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both persisting environmental contaminant and antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority such as clinical settings and spacecraft assembly facilities cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of key knowledge gaps by providing genomic insights into a rare multi-drug resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help evaluate the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings. HighlightsO_LICleanrooms-derived A. johnsonii genomes show favorable traits for increased adaptability C_LIO_LIGenomic signatures of A. johnsonii persisted in the cleanrooms for >10 years C_LIO_LIblaOXA is ubiquitously found in the genome of all A. johnsonii C_LIO_LIE154408A is the first patient colonization by carbapenem-resistant A. johnsonii in Europe C_LI

genomics↗

bioRxiv2025

Emergence of Dual β-lactam and Colistin Resistance via blaFRI-8 and mcr10.2 co-carriage on an IncFII Family Plasmid in Enterobacter vonholyi

ObjectivesEnterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) blaFRI-8, mcr-10.2. isolated from a clinical rectal swab. E323169 is one of only 12 available E. vonholyi genomes. To date, and across over two million pathogenic genomes scanned, only three harbour blaFRI-8 and two encode mcr-10.2, yet none exhibit both genes together. This study analyzes the genomic, phenotypic and epidemiological importance of this rare co-occurrence. MethodsSpecies-ID for E323169 was assigned by MALDI-TOF and then re-assigned and confirmed using a multifactorial genomic workflow. Antimicrobial susceptibilities were determined by MIC assay. The genome of E323169 was sequenced on an Illumina-NextSeq-1000, assembled, and annotated for ARGs, virulence factors, and plasmid replicons detection. Comparative phylogenomics used 12 E. vonholyi RefSeq assemblies, and NCBI metadata were analysed for plasmid distributions of blaFRI-8 and mcr-10.2. ResultsE323169 carried six ARGs: four chromosomally encoded (blaACT-91, fosA, oqxA10, oqxB9) and two plasmid-borne (blaFRI-8 and mcr-10.2) co-located on IncFII(p14)_1_p14 replicon. Additional plasmid replicons: Col(MG828)_1 and ColRNAI_1 were also identified. By mining the NCBI Pathogen Detection pipeline, we identified blaFRI-8 on IncFII replicon in E. asburiae JBIWA002, and mcr-10.2 on a multi-replicon (IncFIB/IncFII) plasmid in E. kobei 11778-yvys. ConclusionThis report documents the first E. vonholyi isolate co-harboring blaFRI-8 and mcr-10.2 on a single IncFII family plasmid, showing the widening host range of plasmid-mediated resistance to carbapenems/colistin. No prior similar co-occurrences reported, underscoring its rarity. These findings highlight the urgent need for enhanced clinical screening and genomic surveillance to curb the spread.

microbiology↗